ARB
Functions | Variables
ad_spec.cxx File Reference
#include "NT_local.h"
#include "map_viewer.h"
#include <dbui.h>
#include <awt_www.hxx>
#include <awt_canvas.hxx>
#include <aw_awars.hxx>
#include <aw_msg.hxx>
#include <aw_root.hxx>
#include <arb_progress.h>
#include <arb_defs.h>
#include <cctype>
Include dependency graph for ad_spec.cxx:

Go to the source code of this file.

Functions

void NT_count_different_chars (AW_window *, GBDATA *gb_main)
 
void NT_create_sai_from_pfold (AW_window *aww)
 
void launch_MapViewer_cb (GBDATA *gbd, AD_MAP_VIEWER_TYPE type)
 

Variables

static const char *const SAI_COUNTED_CHARS = "COUNTED_CHARS"
 

Function Documentation

void NT_count_different_chars ( AW_window ,
GBDATA gb_main 
)
void NT_create_sai_from_pfold ( AW_window aww)

Creates an SAI from protein secondary structure of a selected species.

Parameters
[in]awwAW_window

The function takes the currently selected species and searches for the field "sec_struct". A new SAI is created using the data in this field. A simple input window allows the user to change the default name ([species name]_pfold) for the new SAI.

Note
The import filter "dssp_all.ift" allows for importing the amino acid sequence as well as the protein secondary structure from a dssp file and the structure is stored in the field "sec_struct". That way, secondary structure can be aligned along with the sequence manually and can later be extracted to create an SAI.
Attention
The import filter "dssp_2nd_struct.ift" extracts only the protein secondary structure which is stored as alignment data. SAIs can simply be created from these species via move_species_to_extended().

Definition at line 116 of file ad_spec.cxx.

References AW_window::activate(), aw_input(), aw_message(), AW_root::awar(), AWAR_SAI_NAME, AWAR_SPECIES_NAME, error(), GB_await_error(), GB_begin_transaction(), GB_child(), GB_copy_dropProtectMarksAndTempstate(), GB_CREATE_CONTAINER, GB_create_container(), GB_delete(), GB_end_transaction_show_error(), GB_entry(), GB_FIND, NT_global::gb_main, GB_nextChild(), GB_read_key(), GB_read_string(), GB_read_type(), GB_search(), GB_write_string(), GBS_global_string_copy(), GBT_find_SAI_rel_SAI_data(), GBT_find_species(), GBT_gen_accession_number(), GBT_get_default_alignment(), GBT_get_SAI_data(), GBT_write_string(), AW_window::get_root(), GLOBAL, NT_create_extendeds_window(), NULp, AW_awar::read_string(), and AW_awar::write_string().

Referenced by popup_new_main_window().

void launch_MapViewer_cb ( GBDATA gbd,
AD_MAP_VIEWER_TYPE  type 
)

Variable Documentation

const char* const SAI_COUNTED_CHARS = "COUNTED_CHARS"
static

Definition at line 28 of file ad_spec.cxx.